From 846f68460dd64776a2a3d7101600e473bf70bc1c Mon Sep 17 00:00:00 2001
From: Leon Rauschning <99650940+lrauschning@users.noreply.github.com>
Date: Tue, 10 Dec 2024 11:38:47 +0800
Subject: [PATCH] switch to pip install from git

---
 .github/workflows/build.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
index b556b4b..8f2133f 100644
--- a/.github/workflows/build.yml
+++ b/.github/workflows/build.yml
@@ -28,11 +28,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip setuptools
-        # apparently the runners all have conda installed
-        # use that to install syri, as it isn't on pypi
-        # manually install syris dependencies, conda does not install
-        pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
-        $CONDA/bin/conda install --freeze-installed --no-deps -c conda-forge -c bioconda "syri>=1.6.5"
+        # manually install syris dependencies
+        # seems to be no longer necessary with github install
+        #pip install Cython numpy pandas scipy psutil igraph longestrunsubsequence pysam pulp
+        # manually use pip to install syri from github, as it isn't on pypi
+        pip install git+https://github.com/schneebergerlab/syri.git#egg=syri
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Build package
       run: pip install .